I figure if it works for clothing where the seam is going to be getting a lot more stress and rubbing,(like armholes, crotch seams. . .) it should be fine in a quilt that once you bind and quilt it, there is going to be way less stress on that seam. Yes, it may "weaken" it, but I doubt anyone has done any testing to quantify the difference.
I do this a lot with my very small pieced blocks. Unless I'm not careful and snip the seam, I've never had it be an issue.
However I do try to plan and press seams so I don't need to do this, but sometimes with the small blocks, it's not possible if you want to avoid a big bump of seams coming together.